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Fix run merging for unmerged PE data
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afb66e445f
commit
a5f4fc42d5
2 changed files with 6 additions and 3 deletions
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@ -162,7 +162,7 @@ process {
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}
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withName: CAT_FASTQ {
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ext.prefix = { "${meta.id}-${meta.run_accession}" }
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ext.prefix = { "${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/run_merging/" },
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mode: params.publish_dir_mode,
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@ -139,7 +139,11 @@ workflow TAXPROFILER {
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meta_new.remove('run_accession')
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[ meta_new, reads ]
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}
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.groupTuple()
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.groupTuple(by: 0)
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.map {
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meta, reads ->
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[ meta, reads.flatten() ]
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}
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.branch {
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// we can't concate files if there is not a second run, we branch
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// here to separate them out, and mix after
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@ -151,7 +155,6 @@ workflow TAXPROFILER {
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.mix( ch_reads_for_cat_branch.skip )
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.map {
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meta, reads ->
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[ meta, [ reads ].flatten() ]
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}
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